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DD_1D-SRA/CODE/DATASET/generate_dataset.py
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generate_dataset.py
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# Create LAMMPS files to generate DEM dataset
# Also creates a batch file to execute to launch all the computation
import numpy as np
import os
import pathlib
ref_path = str(pathlib.Path(__file__).parent.resolve()) + r'\ref_lammps'
# PARAMETERS
# Location of data set
path = r'C:/Travail/EPFL/Cours/M2/Projet CSE/LAMMPS/Test'
# List of confinement pressures
P_min = 10e3
P_max = 210e3
P_step = 10e3
conf_Ps = np.arange(P_min,P_max,P_step)
# Initial size of box before confinement
box_size = 0.10
# Size of each subregion of the box (for particle insertion)
region_size = 0.0025
# Number of data points per confinement pressure
dataset_size = 1000
# Maximum deformation of the box
max_deformation = 0.1
# Random seed
np.random.seed(42)
def create_lammps_files(path, conf_P, box_size, region_size):
"""
Write LAMMPS files
"""
path_p = path + '/P={}Pa'.format(conf_P)
if not os.path.exists(path_p):
os.makedirs(path_p)
with open(os.path.join(ref_path, 'ref_lammps_generate.txt')) as f:
lines_ref = f.readlines()
ref_part0 = lines_ref[:8]
ref_part1 = lines_ref[8:29]
ref_part2 = lines_ref[29:40]
ref_part3 = lines_ref[40:]
line_pressure = 'variable confinement_pressure equal {}'.format(conf_P)
line_box = 'region reg block 0.0 {size} 0 {size} -0.0005 0.0005 units box'.format(size=box_size)
nb_regions = int(box_size/region_size)
seeds = np.random.randint(1,1000,nb_regions)
steps = [region_size*i for i in range(nb_regions+1)]
region_lines = []
group_lines = []
fix_lines = []
unfix_lines = []
for i in range(nb_regions):
line1 = 'region region_gouge_{} block 0.00 {} '.format(str(i+1),str(box_size))
line2 = '{:.4f} {:.4f} -0.0005 0.0005 units box'.format(steps[i],steps[i+1])
region_lines.append(line1+line2)
line3 = 'group nve_group region region_gouge_{}'.format(str(i+1))
group_lines.append(line3)
line4 = 'fix ins_{nb} nve_group pour 50000 1 {seed} region region_gouge_{nb} vol 0.2 200 diam poly 2 0.0025 0.5 0.0035 0.5'.format(nb=str(i+1), seed=seeds[i])
fix_lines.append(line4)
line5 = 'unfix ins_{}'.format(str(i+1))
unfix_lines.append(line5)
with open(path_p + '/1_generate_conf_{}Pa.in'.format(conf_P), 'w') as f:
for line in ref_part0:
f.write(line)
f.write(line_box)
f.write('\n')
f.write(line_pressure)
f.write('\n')
for line in ref_part1:
f.write(line)
for line in region_lines:
f.write(line)
f.write('\n')
f.write('\n')
for line in group_lines:
f.write(line)
f.write('\n')
f.write('\n')
for line in fix_lines:
f.write(line)
f.write('\n')
f.write('\n')
for line in ref_part2:
f.write(line)
for line in unfix_lines:
f.write(line)
f.write('\n')
f.write('\n')
for line in ref_part3:
f.write(line)
with open(os.path.join(ref_path, 'ref_lammps_shear.txt')) as f:
lines_shear = f.readlines()
line_1 = 'read_restart confined.restart \n\n'
line_2 = 'variable nb_points equal {} \n'.format(dataset_size)
line_3 = 'variable eps_max equal {} \n'.format(max_deformation)
with open(path_p + '/2_shear.in', 'w') as f:
f.write(line_1)
f.write(line_2)
f.write(line_3)
for line in lines_shear:
f.write(line)
def prepare_simulation(path, conf_Ps, box_size, region_size):
"""
Write LAMMPS files and batch file to start computation
"""
loc = 'cd ' + path + '/P={}Pa'
lmmps1 = 'lmp -in 1_generate_conf_{}Pa.in'
lmmps2 = 'lmp -in 2_shear.in'
with open(path + '/start_DEM.bat', 'w') as f:
for conf_P in conf_Ps:
conf_P = int(conf_P)
create_lammps_files(path, conf_P, box_size, region_size)
f.write(loc.format(conf_P))
f.write('\n')
f.write(lmmps1.format(conf_P))
f.write('\n')
f.write(lmmps2)
f.write('\n')
# Check if required reference files exist
for file in ['ref_lammps_generate.txt','ref_lammps_shear.txt']:
if not os.path.exists(os.path.join(ref_path, file)):
raise Exception(f'Missing reference file: {file}')
# Start file writing
prepare_simulation(path, conf_Ps, box_size, region_size)
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